Preheat the oven to 350°F and line two 12-cup muffin pans with 18 paper liners.
In a medium bowl, whisk together the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.
In a separate bowl, mix the pumpkin puree, granulated sugar, brown sugar, vegetable oil, eggs, and vanilla extract until smooth.
Gradually add the dry ingredients to the pumpkin mixture, stirring just until combined. Do not overmix.
In another bowl, beat the softened cream cheese, granulated sugar, egg yolk, vanilla extract, and flour until smooth and creamy.
Fill each muffin cup about halfway with pumpkin batter. Add a spoonful of the cheesecake mixture to the center of each muffin.
Mix the flour, brown sugar, cinnamon, salt, and melted butter for the streusel until crumbly. Sprinkle the streusel over each muffin.
Bake for 20 to 22 minutes, or until the muffins are set and a toothpick inserted into the pumpkin portion comes out clean.
Cool the muffins in the pan for 5 minutes before transferring them to a wire rack to cool completely.